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academic/samtools: Updated for version 1.11.

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Signed-off-by: Dave Woodfall <dave@slackbuilds.org>

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
This commit is contained in:
Rob van Nues 2020-10-09 01:58:08 +01:00 committed by Willy Sudiarto Raharjo
parent 2fd6e68c6d
commit 91bffe057f
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GPG key ID: 3F617144D7238786
3 changed files with 20 additions and 20 deletions
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28
academic/samtools/README
View file

@ -1,16 +1,16 @@
SAM (Sequence Alignment/Map) format is a generic format for storing large
nucleotide sequence alignments. The original samtools package has been split
into three separate but tightly coordinated projects: htslib (C library for
handling high-throughput sequencing data), samtools (for handling SAM, BAM,
CRAM), and bcftools (for handling VCF and BCF).
SAM (Sequence Alignment/Map) format is a generic format for storing
large nucleotide sequence alignments. The original samtools package has
been split into three separate but tightly coordinated projects: htslib
(C library for handling high-throughput sequencing data), samtools (for
handling SAM, BAM, CRAM), and bcftools (for handling VCF and BCF).
Samtools is now distributed as an individual package. Installation is set up
so that the code uses an external HTSlib (also at SBo). Although deprecated
upstream, in the case that people need parts of samtools-legacy (e.g header
files or libbam) these can be installed from this package by modifying the
samtools.Slackbuild. Note that the sam.h of htslib differs from sam.h coming
with samtools.
Samtools is now distributed as an individual package. Installation is
set up so that the code uses an external HTSlib (also at SBo). Although
deprecated upstream, in the case that people need parts of
samtools-legacy (e.g header files or libbam) these can be installed from
this package by modifying the samtools.Slackbuild. Note that the sam.h
of htslib differs from sam.h coming with samtools.
Prior to the introduction of HTSlib, SAMtools and BCFtools were distributed
in a single samtools-0.1.x package. This old version remains available from
SBo as samtools-legacy.
Prior to the introduction of HTSlib, SAMtools and BCFtools were
distributed in a single samtools-0.1.x package. This old version remains
available from SBo as samtools-legacy.

4
academic/samtools/samtools.SlackBuild
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@ -23,7 +23,7 @@
# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
PRGNAM=samtools
VERSION=${VERSION:-1.10}
VERSION=${VERSION:-1.11}
BUILD=${BUILD:-1}
TAG=${TAG:-_SBo}
@ -117,7 +117,7 @@ mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
cp -a \
AUTHORS LICENSE README INSTALL NEWS examples \
$PKG/usr/doc/$PRGNAM-$VERSION
cp $CWD/README.references $PKG/usr/doc/$PRGNAM-$VERSION
cp $CWD/README $PKG/usr/doc/$PRGNAM-$VERSION
cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
mkdir -p $PKG/install

6
academic/samtools/samtools.info
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@ -1,8 +1,8 @@
PRGNAM="samtools"
VERSION="1.10"
VERSION="1.11"
HOMEPAGE="http://www.htslib.org"
DOWNLOAD="https://github.com/samtools/samtools/releases/download/1.10/samtools-1.10.tar.bz2"
MD5SUM="506b0b9b2628e1f3bbedd77855b4c709"
DOWNLOAD="https://github.com/samtools/samtools/releases/download/1.11/samtools-1.11.tar.bz2"
MD5SUM="9fd052652a9ceb56fc1098e63f596330"
DOWNLOAD_x86_64=""
MD5SUM_x86_64=""
REQUIRES="htslib"